THE EVOLUTION LIST

THE EVOLUTION LIST is a forum for commentary, discussion, essays, news, and reviews that illuminate the theory of evolution and its implications in original and insightful ways. Unless otherwise noted, all materials may be quoted or re-published in full, with attribution to the author and THE EVOLUTION LIST. The views expressed herein do not necessarily reflect those of Cornell University, its administration, faculty, students, or staff.

The answer is that this long-term research project has provided direct evidence for the initial stages of macroevolution in the field. To be precise, what is at issue in the research reported by the Grants is what is known as “secondary contact”. This is what happens after a sub-population has become reproductively isolated from the population from which it was derived. According to Theodosius Dobzhansky and Ernst Mayr (two of the founders of the “modern evolutionary synthesis”), speciation is the result of genetic isolation resulting from geographic isolation: the members of two geographically separated populations of organisms no longer interbreed, and therefore genetic differences between the two populations accumulate over time.

This process, commonly known as allopatric speciation, can be considered to consist of six discrete, successive stages:

2) Divergence: The genomes of the members of the vicariant subpopulation diverge from the genomes of the members of the panmictic source population as the result of various genetic mechanisms (for a list of such mechanisms, click here);

3) Reproductive Isolation: The reproductive anatomy, physiology, and behavior of the members of the vicariant subpopulation diverge from the reproductive anatomy, physiology, and behavior of the members of the original source population, resulting in reproductive isolation and (eventually...at least sometimes) reproductive incompatibility;

4) Secondary Contact: Successful hybridization between members of the diverging sub-population and the original source population decreases in frequency as the result of pre-zygotic and post-zygotic isolating mechanisms (for more, click here);

This is the theoretical model; what actual empirical studies have shown is that diverging phylogenetic lines frequently become reintegrated, separating and then re-integrating more than once. Sometimes they become sufficiently reinforced that they remain separate and diverge continuously, and sometimes they “collapse” back into a single, panmictic “species”.

The importance of all of this to the theory of macroevolution is that divergence is divergence: phylogenetic divergence via reproductive isolation is macroevolution. Speciation is simply the first stage in the origin of all higher taxa.

Therefore, what is ultimately at issue between evolutionary biologists and creationists (including most ID supporters) is not speciation per se nor the mechanisms by which it occurs or is reinforced, but rather whether there are “natural” limits to the degree of divergence that can take place as a result of the mechanisms that comprise the “engines of variation”.

Despite much posturing on both sides, this is not a question that can be answered via pure theoretical (i.e. mathematical) speculation. However compelling a theoretical model may appear, it must be tested empirically to see if it conforms to the evidence from nature. This is what evolutionary biologists do all the time, and what ID theorists seem either unable or unwilling to do. Until this situation changes (if it ever does), no reputable empirical scientist anywhere will ever take ID seriously.

Admittedly, I have written recently that the "modern evolutionary synthesis" is dead (see here for more), but in doing so I have taken pains to point out that the theory of evolution itself is most assuredly not dead. On the contrary, it is very much alive. Indeed, it has never been more vigorous than it is today.

But that's not what the creationists are saying. What they're saying (or trying to say) is that the whole concept of evolution itself is dead: the Earth and everything on it was created a relatively short time ago, and even if life on Earth has changed (a little), all of that change has been guided by the deity of the Abrahamic religions (Judaism, Christianity, Islam, Mormonism, etc.) Indeed, just this morning a new podcast was launched at the website of the Discovery Institute, in which neo-Paleyist and ID creationist John West asserts once again that "Darwinism is dead".

Is this news? And is it new? How long have creationists been predicting the demise of Darwin's theory of evolution? Apparently, they've been doing so since a few decades before Darwin published it. G. R. Morton has compiled a short list of quote from creationists predicting the impending overthrow of the theory of evolution (you can read it here). He introduces his anthology of science denialism with this:

In recent reading of [Dr. William] Dembski and other ID proponents I saw them make a claim which has been made for over 40 years. This claim is one that the young-earthers have been making. The claim is that evolution (or major supporting concepts for it) is increasingly being abandoned by scientists, or is about to fall. This claim has many forms and has been made for over 162 years. This is a compilation of the claims over time. The purpose of this compilation is two-fold. First, it is to show that the claim has been made for a long, long time. Secondly, it is to show that entire careers have passed without seeing any of this movement away from evolution. Third, it is to show that the creationists are merely making these statements for the purpose of keeping hope alive that they are making progress towards their goal. In point of fact, no such progress is being made as anyone who has watched this area for the last 40 years can testify. The claim is false as history and present-day events show, yet that doesn't stop anyone wanting to sell books from making that claim.

Morton's quotations from creationists begins with a quote dating to 1825, 34 years before Darwin published the Origin of Species. Apparently, what many historians have asserted was true: that the idea of evolution was "in the air" in the mid-19th century, and that Darwin simply codified and provided evidence for an idea that was already becoming generally well-known and at least partially accepted. The fact that Alfred Russell Wallace came up with the same mechanism that Darwin did for descent with modification — natural selection — is further evidence for the idea that evolution was "in the air" at the time.

It still is, and even moreso. Not only has the theory of evolution not "crumbled", it is currently undergoing its most rapid expansion since 1859. Darwin's original theory was limited strictly to biological evolution, but now his theory is being extended into astrophysics, geology, economics, psychology, sociology, and even literature and art history. It is this tremendous success that upsets the opponents of Darwin's theory, and that impels them (in the face of overwhelming evidence to the contrary) that the most widely accepted, most generally applicable, and most analytically powerful theory in all of science is on its way out.

In other words (and true to their creationist roots), they stare reality in the face and deny it.

Well, the appointed day (19 November) for Ray's distribution of the Origin came and went, but apparently no creationists showed up at Cornell to pass out Ray's "abridged" copy of the Origin of Species with Ray's laughably mendacious introduction. I really wanted to get a copy, eagerly pressed into my grasp by the hot little hands of a freshly scrubbed creationist, but after checking every likely location — from Ho Plaza in front of the Straight (where there were a few empty folding tables, sitting forlornly in the rain) to the plaza between Olin and Uris libraries (where a few damp smokers contemplated "The Song of the Vowels") to Trillium (where Cornell's elite meet to eat) to Mann Library (the second largest agriculture and biology library in the world...where is the first, exactly?) to Appell Commons (where you can work up a sweat before downing your stir fry)...nada, nobody, zip, just grey sky and freezing rain. And so my quest for another artifact from the culture wars went unsatisfied...

By the way, Ray Comfort has apparently been making a career out of lying lately, asserting that his version of the Origin would be passed out at Cornell yesterday, and that his bastardized version would be available in its entirety. Although I didn't get my copy, I have been informed by people at other academic institutions who did that, on the contrary, he's apparently cut out precisely those chapters that have proven most inconvenient for creationists in the past. And, he's added a fifty-page "introduction" that's filled with laughably inaccurate so-called "arguments" against the content of Darwin's masterpiece.

Furthermore, his apparently false claim that he was printing 170,000 copies of his version of the Origin was apparently intended to push his version to the top of Amazon.com's search results for the Origin of Species, where members of the uninformed public who were interested in reading Darwin's masterpiece during this bicentennial year (it's the 200th anniversary of Darwin's birth and the 150th anniversary of the first publication of the Origin of Species) would innocently buy his bastardized version with his mendacious introduction. A clever public relations gambit — gaming Amazon.com's popularity algorithm — but I guess he forgot about the reviewer's comments at Amazon, where his lying and propaganda techniques and public relations tricks have been exposed by people more interested in the truth than making money by shilling for Jesus (who would have been horrified by Ray's tactics, and probably by his theology as well).

Thursday, November 19, 2009

The Modern Synthesis is Dead - Long Live the Evolving Synthesis!

It has been almost exactly a century and a half since Darwin's Origin of Species was first published, and half a century since the conference at the University of Chicago where the "triumph" of the "modern evolutionary synthesis" was celebrated. So, isn't it a little odd that some well-respected scientists and historians of science are proclaiming in this celebratory year that the modern evolutionary synthesis is dead?

For example, Eugene Koonin, senior investigator at the National Center for Biotechnology Information, National Library of Medicine, and National Institutes of Health in Bethesda, Maryland, has published two essays on the current status of the "modern evolutionary synthesis":

The Origin at 150: Is a new evolutionary synthesis in sight?Trends in Genetics, 25(11), November 2009, pp. 473-475.

Abstract: The 200th anniversary of Charles Darwin and the 150th jubilee of the On the Origin of Species could prompt a new look at evolutionary biology. The 1959 Origin centennial was marked by the consolidation of the modern synthesis. The edifice of the modern synthesis has crumbled, apparently, beyond repair. The hallmark of the Darwinian discourse of 2009 is the plurality of evolutionary processes and patterns. Nevertheless, glimpses of a new synthesis might be discernible in emerging universals of evolution.

ABSTRACT: Comparative genomics and systems biology offer unprecedented opportunities for testing central tenets of evolutionary biology formulated by Darwin in the Origin of Species in 1859 and expanded in the Modern Synthesis 100 years later. Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected. Major contributions of horizontal gene transfer and diverse selfish genetic elements to genome evolution undermine the Tree of Life concept. An adequate depiction of evolution requires the more complex concept of a network or 'forest' of life. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation. Several universals of genome evolution were discovered including the invariant distributions of evolutionary rates among orthologous genes from diverse genomes and of paralogous gene family sizes, and the negative correlation between gene expression level and sequence evolution rate. Simple, non-adaptive models of evolution explain some of these universals, suggesting that a new synthesis of evolutionary biology might become feasible in a not so remote future.

A big deal, right? Well, not really. Will Provine and I have been saying that “the modern evolutionary synthesis is dead” for years. Indeed, Will Provine coined the phrase “the hardening of the synthesis” to describe the narrowing of focus in evolutionary theory during the first half of the 20th century to concepts entirely reducible to mathematical models, especially theoretical population genetics.

Ironically, Dr. John Sanford and Dr. William Dembski (among others in the ID camp) have not moved beyond this narrow focus on theoretical population genetics, and so have apparently missed the fact that evolutionary biology has evolved far beyond the narrow theoretical focus of the mid-20th century. Some ID supporters have also suggested that Dr. Koonin might be taking a “big career risk” in stating the obvious. I don't think so. On the contrary, what Dr. Koonin has pointed out is that evolutionary biology today is broader, more generally applicable, and less narrowly focused than at any time since the publication of the Origin of Species 150 years ago. Being an evolutionary biologist today is like being a physicist in 1905 — a whole new world of theoretical and practical empirical research is opening up, with new discoveries being made every day.

As just one example, Kyoto-prize-winning evolutionary biologists Peter and Rosemary Grant have reported on something that Darwin could only speculate about: the systematic empirical documentation of the “origin” of a new species (reported here yesterday). Creationists have of course moved the goalposts, arguing that they accepted all along that new species could arise from existing ones, it’s just microevolution, which of course everyone accepts. This, despite the fact that speciation has always been considered to be the first (and perhaps most important) stage in macroevolution, and that less than two decades ago creationists were confidently stating that “true” speciation had not only never been observed, it couldn’t ever be observed because it can’t happen.

Now the leaders of the ID movement — people like Dr. Michael Behe and Dr. William Dembski — publicly state that they fully accept that descent with modification from common ancestors (i.e. evolution) has happened, that microevolution (i.e. natural selection, sexual selection, and genetic drift) are also fully supported by the evidence, and that the “real” focus of disagreement is over the “engines of variation” that produce the raw material upon which the “engines of evolution” operate. They’ve come a long way, but they’ve missed the parade by a couple of decades. So it goes…

I would say that Dr. Koonin's essays on where evolutionary biology is today are quite close to the the mark. The concept of natural selection as the foundation of evolutionary change has been largely superseded, mostly through the work of Motoo Kimura, Tomoko Ohta, and others, who have shown both theoretically and empirically that natural selection has little or no effect on the vast majority of the genomes of most living organisms.

However, ID supporters should find this sea change in evolutionary biology to be cold comfort. The overall effect of the advances in our understanding of how genomes and phenotypes change over time has had the same effect on evolutionary theory that the rise of quantum mechanics had on classical physics. Einstein famously asserted that “God does not play dice”, but a century of physics research has shown him to be more wrong about how the universe works at the quantum level than ever.

The same is true for the “evolving synthesis”. Rather than revert to a neo-Paleyan paradigm (as proposed by Behe, Dembski, and their supporters), evolutionary biology has gone in the opposite direction, the same direction that quantum mechanics has taken. According to the “modern synthesis” of the last century, the genome was “homeostatic”, “organized”, and “regulated” primarily by natural selection. Sure there were purely random processes also going on (such as genetic drift), but most evolutionary change was both adaptive and coherent over time.

Here's what Dr. Koonin writes (see above):

"There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a nonadaptive consequence of evolution under weak purifying selection rather than an adaptation."

Kimura, Ohta, Jukes, and Crow dropped a monkey wrench into the "engine" at the heart of the modern synthesis — natural selection — and then Gould and Lewontin finished the job with their famous paper on “the spandrels of San Marco and the Panglossian paradigm”. The rise of evo-devo over the past two decades has laid the groundwork for a completely new and empirically testable theory of macroevolution, a theory that is currently facilitating exponential progress in our understanding of how major evolutionary transitions happen. And iconoclasts like Lynn Margulis, Eva Jablonka, Marian Lamb, Mary Jane West-Eberhard, and David Sloan Wilson are rapidly overturning our understanding of how evolutionary change happens at all levels, and how it is inherited.

So, as I have said many times before, when ID supporters set their sights on “neo-Darwinism” as a target for criticism, they set their sights on a model that has been all but abandoned. The carnival has moved on and ID supporters are fighting battles that evolutionary biologists left behind a half century and more ago.

And so, on this 150th anniversary of the publication of Darwin's Origin of Species, evolutionary biologists can raise a frosty glass and say

The Darwinian Revolution To Be Shown at Cornell

There will be a free public showing of The Darwinian Revolution video series at 4 PM on Tuesday 24 November 2009 in the large classroom (room 3330) of the Tatkon Center in Balch Hall. This presentation will take place on the 150th anniversary of the publication of Charles Darwin's Origin of Species, and is part of Cornell's celebration of the Darwin Bicentennial. The host of the video series, Cornell evolutionary biologist Allen MacNeill, will be on hand at the presentation to discuss the videos and answer questions about evolutionary biology in general, and about The Darwinian Revolution video series in particular.

The Darwinian Revolution is a series of six videos addressing the content and history of the theory of evolution. Produced by Cornell's CyberTower program and hosted by evolutionary biologist Allen MacNeill, the six-part series includes an overview of evolutionary biology, a history of the concept of evolution in western civilization, a brief consideration of Lamarck's theory of evolution via the inheritance of acquired characteristics, a detailed look at Darwin's theory of evolution by natural selection, a brief exploration of Mendel's theory of particulate inheritance and its role in the origins of the "modern evolutionary synthesis", and a look forward at the future prospects for evolutionary biology. The series was videotaped at the Museum of the Earth in Ithaca, New York, and features interviews with museum director and paleontologist Warren Allman and Cornell historian of science William Provine.

This public showing of The Darwinian Revolution is free and open to the general public. It is cosponsored by Cornell's CyberTower program, in cooperation with the Museum of the Earth and Cornell's Tatkon Center as part of this year's celebration of the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of Darwin's Origin of Species.

The Darwinian Revolution video series can also be viewed online here. For more information about the video series, go here.

Wednesday, November 18, 2009

A New Species of Finch may have Evolved in the Galapagos

As I have noted in several recent blogposts, Charles Darwin's Origin of Species was published 150 years ago this month. One of Darwin's crucial examples of descent with modification in the Origin was the evolutionary diversification of a group of finches now usually referred to as "Darwin's finches". In the Origin Darwin did not speculate as to how long this evolutionary diversification took place, except to suggest that it would require "the passage of long ages". However, in a private letter to one of his correspondents, Darwin suggested that it would take at least fifty years to see unambiguous effects of natural selection.

"It was in 1981, that the Grants spotted an unusually heavy medium ground-finch (Geospiza fortis). At 29.7 grams, the male was more than 5 grams heavier than any they had seen on Daphne Major before. Genetic analysis showed that it probably came from the neighbouring island of Santa Cruz.

The Grants numbered the bird 5110 and followed it and all its known descendants over seven generations. Many of its descendants stuck out from the other G. fortis on Daphne Major: they had unusually shaped beaks and their songs differed from those of the other finches.

...

In the fourth generation, a severe drought hit the island and 5110's descendants were reduced to one male and one female — a brother and sister. From then on the immigrant lineage isolated itself, breeding with no other G. fortis on the island....

"No study of this sort has been done before, and it shows one way in which speciation can get started," say the Grants from Japan, where they are receiving the Kyoto Prize for basic science for their life work."

Several further points from the Grants' report are significant. Many evolutionary biologists (including Tijs Goldschmidt) have speculated that sexual selection may be a significant cause of evolutionary diversification, including the origin of new species as the result of female choice. It appears that sexual selection has played an important part in the differentiation of the incipient species of finch on Daphne Major:

"The fact that 5110's descendants haven't mixed could be because they differ from the natives. The Grants note that the descendants have a differently shaped beak from those native to Daphne Major. As finch beaks are vital in identifying potential mates, this could serve to keep them reproductively isolated.

5110's offspring also have the avian equivalent of a strange accent. These finches learn their songs from their father, and the Grants suggest that 5110 sang the songs from his birth home of Santa Cruz then modified his come-hither ballad by roughly copying the Daphne Major birds'. This imperfect copying, they suggest, has over time acted as a barrier to interbreeding.

Also, the Grants' research has illustrated an important point concerning Darwinian speciation. As Darwin pointed out in the Origin, the distinction between varieties, subspecies, and species are "entirely arbitrary", and ultimately depend on reproductive isolation:

"The Grant's aren't yet ready to call 5110's lineage a new species, a term fraught with difficulty for evolutionary biologists. "There is no non-arbitrary answer to the question of how many generations should elapse before we declare the reproductively isolated lineage to be a new species," they say. "For the present it is functioning as a [separate] species because its members are breeding only with each other."

The Grants think there is only a small chance that 5110's descendants will remain isolated long enough to speciate. If they do, the new species will have to be named: "When discussing these birds we call them 'big birds'," the Grants say. "That could be translated into Latin."

Finally, the observation that this incipient species of finch resulted from the consanquineous mating of a pair of full siblings lends support to my proposal that speciation can be facilitated by first degree inbreeding. Here's what I wrote about this proposal on Thanksgiving in 2006:

"Wouldn't [the genetic rearrangements usually accompany reproductive isolation] have to occur within at least two members- one male, one female- of the same population in order for it to have any chance of getting passed on? And therefore, wouldn't this make such genetic rearrangements difficult, if not impossible to pass on?"

To which I answered:

No. All that would need to happen to make this possible would be for two first-degree relatives carrying the genetic rearrangement to mate and have offspring. First degree relatives (i.e. parents and offspring or full siblings) can easily have the same chromosomal mutation (i.e. a fusion, fission, translocation, or inversion), as they would inherit it from a single parent. If they were to mate with each other (a not uncommon event among non-humans...and even among some humans), they would be able to produce fertile offspring carrying the same chromosomal mutation.

Yes, it is true that first degree mating carries with it the possibility of reinforcement of recessive lethal alleles. However, as many geneticists and evolutionary biologists have repeatedly pointed out, this is actually beneficial to the population within which such reinforcement happens, as the alleles are "purged" from the population as a result.

In other words, mating between first degree genetic relatives within a small, isolated population would have the effect of both removing deleterious alleles from the population and allowing chromosomal mutations to spread throughout the population, especially if such mutations were at all beneficial (although they would diffuse almost as well if they were selectively neutral, as would probably be the case given that no change in overall genetic information would have occurred).

Furthermore, the hypothesis that I have presented above squares very well with the currently prevailing theory of speciation: that of peripatric speciation, as first proposed by Ernst Mayr. According to Mayr's theory, speciation occurs most often in small, isolated populations on the periphery of large, panmictic populations. There is abundant natual history evidence that this is the case, especially in animals.

However, to my knowledge no one has yet proposed a mechanism explaining how peripatric speciation would come to be associated with the kinds of chromosomal changes that are commonly associated with reproductive isolation and speciation. My hypothesis – that first-degree inbreeding facilitates chromosomal speciation – is an attempt to reconcile those two observations.

In a large, panmictic population, selection would tend to eliminate individuals who mate with first-degree relatives as a result of decreased viability due to inbreeding depression and the increased frequency of expression of homozygous lethal alleles.

However, in very small, isolated populations individuals who occasionally mate with first degree relatives (i.e. "facultative first degree inbreeders") could easily have a selective advantage of individuals who avoid mating with first degree relatives (i.e. "obligate outbreeders").

Males in particular would tend to loose less as the result of mating with first degree relatives, as their parental investment in offspring is lower (i.e. they can waste gametes and even zygotes by mating with their first degree relatives, without significantly decreasing their reproductive success).

However, even females can cut their losses by mating with first degree relatives if the likely alternative is failure to mate at all due to unavailability of non-relatives. This would especially be the case in small, isolated populations, which are exactly the kind of populations in which speciation is most likely to occur.

The effects described above would be facilitated by increased genomic homogeneity, such as would result from genetic bottlenecks and founder effects. This is because close inbreeding intensifies genomic homogeneity and decreases genetic variation, especially in isolated populations with decreased gene flow from other populations.

This hypothesis – that first degree inbreeding facilitates chromosomal speciation – immediately suggests a series of predictions, all of which are empirically testable:

• The frequency of mating between first degree relatives should be inversely correlated with effective breeding population size. That is, the smaller the effective breeding population, the greater the frequency of mating between first degree relatives (i.e. “first degree inbreeding”).

• The increased frequency of “first degree inbreeding” in such populations should be more pronounced in males. That is, males should be more likely to attempt mating with first degree relatives, especially in small, isolated populations.

• The frequency of “chromolocal mutations” (that is, chromosomal fission/fusion/inversion/translocation mutations) should also be inversely correlated with effective breeding population size. That is, the smaller the effective breeding population, the greater the frequency of viable “chromolocal mutations.”

• Peripatric speciation events should be correlated with small population size, chromolocal mutations, and first degree inbreeding.

• Speciation resulting from chromolocal mutations should be much less common in large, panmictic populations.

• First degree inbreeding should also be much less common in large, panmictic populations.

• The success rate of artificial (i.e. facilitated/forced) first degree mating should be directly correlated with the degree of inbreeding. That is, the more inbred a population, the more successful artificial first degree inbreeding should be.

• Paleogenomic analysis should find close correlations between genetic bottlenecks, founder events, and peripatric speciation events and the frequency of chromolocal mutations and genetic homogeneity (resulting from first degree inbreeding).

• Relatively large changes in phenotype resulting from chromolocal effects should be more common in small, isolated populations.

• Speciation should be easier (and therefore more frequent) among asexually reproducing eukaryotes, such as plants and parthenogenic animals (among whom aneuploidy is largely irrelevant).

Let me stress two things about the foregoing:

• What I am suggesting is, at this stage, merely a hypothesis, but one that generates a series of immediately testable predictions.

• The hypothesis is, of course, based on the idea that incest (i.e. first degree inbreeding) is the most likely explanation for the diffusion of chromolocal mutations throughout small, isolated populations of animals. Let me stress as strongly as possible that I am NOT advocating incest, I am simply pointing out that first degree inbreeding would facilitate the kind of chromolocal mutations that are often correlated with species differences in animals. The same is also true for plants, of course, but in plants we don't call it "incest," we call it "self-pollination."

At the time that I proposed this hypothesis in November, 2006, I was a little perplexed at why no one has yet proposed this mechanism, given the fact that it is already used as the explanation for speciation in plants via polyploidy. The only explanation that seems reasonable to me is that most evolutionary biologists assume that animals will always avoid mating with first-degree relatives as a result of the increased frequency of inbreeding depression and expression of homozygous lethal alleles that result from it.

However, the Grants' observation of incipient speciation among the finches of Daphne Major, which was apparently facilitated by first-degree inbreeding lends support to my hypothesis.

And that's a reason for me to give thanks next week — Happy Thanksgiving, one and all!

Monday, November 16, 2009

The ID Cookie Crumbles...

During this year of celebration of Darwin and evolutionary biology, Intelligent Design (ID) supporters are fond of asserting that a branch of the biological sciences that currently accounts for over 100 regularly published journals (containing over 1000 peer-reviewed scientific reports) per year, over 1000 books published by reputable scientific publishers per year, and involving grant and foundation support amounting to several billion dollars per year is "crumbling", while ID, which accounts for not one peer-reviewed scientific journal and one peer-reviewed book (published over a decade ago) is replacing it.

I can go to Mann Library here at Cornell (the second largest library of biology in the world, comprising over a million books and bound periodicals) and find the equivalent of an entire floor devoted to evolutionary biology. I couldn't carry this month's issues of the various journals devoted to evolutionary biology to the loan desk, even if I used a large laundry basket and made several trips. I have a paltry selection of the most current books on the subject of evolution in my personal library: only 1000+ volumes published in the past ten years or so. If I had unlimited funds, I could buy ten times as many, and still could not keep up with the field.

Virtually every large university in the world has a department of ecology and evolutionary biology. Here at Cornell we have such a department, with almost two dozen professors and dozens of graduate students, and there are at least five other departments at Cornell who number evolutionary biologists among their members. There are almost half a dozen undergraduate and graduate organizations devoted to the scientific aspects of evolutionary biology at Cornell; branches of such societies are found worldwide.

By contrast, there are two tenured professors in the entire world who explicitly support ID, only one of whom is in a department devoted to an empirical science (the other teaches at a theological seminary). Neither of them is currently engaged in empirical research intended to validate ID.

Wednesday, November 11, 2009

Books in Celebration of the 150th Anniversary of the Origin of Species

2009 marks several important anniversaries in the science of evolutionary biology. Perhaps the two most important are the 200th anniversary of the birth of Charles Darwin and the 150th anniversary of the publication of his most important book, On the Origin of Species, originally published in November of 1859. Scientific societies around the world are celebrating these two events, with “Darwin Day” observances at hundreds of colleges, universities, and museums, including Cornell University and the Museum of the Earth at the Paleontological Research Institution in Ithaca, New York.

Publishers are also celebrating these two anniversaries, bringing out a flood of books on Darwin and evolution. There isn’t space in this blogpost to note all of these publications, but we can mention some of the most noteworthy and relevant of these publications. Here is an annotated list of some of the best and most comprehensive publications that have come out recently, celebrating the life and work of Charles Darwin and his theory of evolution by natural selection. The full publication information for each work is included in this list, followed by a brief paragraph describing its contents.

Perhaps the best way to celebrate Darwin’s life and work is to read his most important and influential books. In preparation for the Darwin bicentennial several publishers have brought out various versions of his books. This one is the best, not only because it includes his four most influential publications, but also because the editor, evolutionary biologist Edward O. Wilson, provides a brief but illuminating introduction to each one. Wilson places Darwin’s work in its historical and scientific context, and shows how each of his four great books laid the groundwork for the modern science of biology. If you only have time for one of these books, let this compendium be the one you read this year.

Darwin, Charles (James T. Costa, editor) (2009) The Annotated Origin: A Facsimile of the First Edition of On the Origin of Species. Belknap Press of Harvard University Press: Cambridge, MA, ISBN 0674032810 (hardcover, $35.00), 576 pages. Available here.

Darwin didn’t originally intend to publish the book we now know as the Origin of Species. He was working on a much longer multi-volume work that he intended to call Natural Selection, and rushed to publish an “abstract” of this work in 1859 to forestall losing his priority for the idea to Alfred Russell Wallace. As a consequence, the Origin of Species has no footnotes, endnotes, nor bibliography. This version of the Origin makes up for that lack. Ably edited by James Costa, The Annotated Origin contains many of the annotations that the original Origin of Species lacked, and provides the reader with a comprehensive grounding in the natural history that Darwin marshaled in support of his revolutionary theory.

Darwin rushed to publish the Origin of Species, and included only one technical illustration in the first edition. This lack of illustrations has been rectified in David Quammen’s beautifully illustrated version of the Origin. Perhaps best known for his masterful book on island biogeography and extinction, The Song of the Dodo, Quammen has chosen a huge selection of images that illuminate Darwin’s theory in ways that Darwin himself would have found both fascinating and extremely valuable for a deeper understanding of his theory.

DARWIN'S BOOKS (online)

The Internet has provided readers and scholars today with an unparalleled opportunity to study the works of Darwin online. By far the best of these electronic resources is a website initiated and maintained by John Van Whye and his colleagues in England. Available online at http://darwin-online.org.uk/, The Complete Works of Charles Darwin includes not only all of Darwin’s books (available in all of their various editions), but also photographic facsimiles of these works side-by-side with searchable full text versions, plus all of Darwin’s scientific publications and a massive and growing collection of his voluminous correspondence. Here is a sampling:Darwin, Charles (1845) Journal of Researches into the Natural History and Geology of the Countries Visited During the Voyage of H.M.S. Beagle Round the World, Under the Command of Capt. Fitz Roy, R.N. 2d edition. John Murray: London, UK, 536 pages. Text and images available here.

This was Darwin’s first and most popular book for the general public, establishing him as the premier naturalist in England at the time of its publication. Continuously in print since 1845, the Voyage of the Beagle (as it is most often referred to) is both a marvelous compendium of natural history and a fascinating journal of a voyage of discovery almost unparalleled in the literature of science.

Darwin, Charles (1859) On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. John Murray: London, UK, 522 pages. Text and images available here.

Darwin’s most important book, and perhaps the most important book ever published in the science of biology. Indeed, a strong argument could be made that this book single-handedly founded the modern science of biology. This online edition juxtaposes the text of the Origin with photographs of the corresponding pages from the first edition.

Darwin, Charles (1871) The Descent of Man, and Selection in Relation to Sex. John Murray: London, UK, 424 pages. Text and images available here.

Darwin’s second most important book, and perhaps the most controversial of his published works, the Descent of Man (as it is most often referred to) contains Darwin’s proposal that humans have evolved from “lower” primates, and a detailed exploration of what Darwin believed to be the most important mechanism in the evolution of humans: sexual selection. Darwin also speculates on the evolutionary origin of such uniquely human traits as art, language, and morality.

Darwin, Charles (1871) The Expression of the Emotions in Man and Animals. John Murray: London, UK, 374 pages. Text and images available here.

One of Darwin’s lesser-known books, but no less important in its own way, The Expression of the Emotions in Man and Animals is often credited with founding the modern science of animal behavior. In it, Darwin explored the biological basis for the expression of emotions in humans and other animals, with detailed examples (many with accompanying photographs) that show how human emotions are most probably derived from the emotions of other “lower” animals, including dogs as well as monkeys and other primates.

DARWIN'S LIFE AND WORK (adults/general)

Many people (including many evolutionary biologists) not only have never read Darwin's books, but also do not know how Darwin came to write them. Furthermore, opponents of Darwin's theories often portray Darwin's life and personal beliefs in as negative a light as possible, in an attempt to discredit his theories. Perhaps the best antidotes to both of these deficiencies are the books listed here, which together provide a comprehensive view of Darwin's life and work. Most of them are written for non-scientists, and all of them provide a fascinating glimpse into the work of the founder of the science of biology.Browne, Janet (1996) Charles Darwin: A Biography, Volume 1: Voyaging. Princeton University Press: Princeton, NJ, ISBN 0691026068 (paperback, $25.95), 622 pages. Available here.

Although not explicitly published in celebration of the Darwin bicentennial, Janet Browne’s two-volume biography of Darwin is widely recognized as the premier biography of the founder of evolutionary biology. This first volume covers Darwin’s youth and early career, up to the completion of the voyage of HMS Beagle and the germination of his theory of evolution by natural selection. Using the extensive collection of Darwin’s correspondence along with personal papers and those of his family and scientific associates, Browne draws a detailed and sometimes surprising portrait of the founder of the most comprehensive and controversial theory in the natural sciences.

In this second volume of Janet Browne’s two-volume biography of Darwin, Janet Browne explores the origin of the Origin of Species and Darwin’s other ground breaking and revolutionary works. Unlike some of Darwin’s other biographers, Browne gets most of the science right in her biography, and illuminates Darwin’s ideas in light of his detailed work in natural history. She also provides insights into Darwin’s personality, including his much-noted reclusive nature, and shows how his scientific work and ideas were influenced by events in his private life.

Although Darwin wrote an autobiography, he never intended it to be a comprehensive history of his life or his ideas. Rather, he did it almost on a lark, as a kind of “gift” to the members of his family and closest friends. Despite this, his autobiography provides some fascinating insights into his personality, and especially his views on art, literature, religion, ethics, and philosophy. This edition includes autobiographical material that was suppressed by Darwin’s widow and son, and should be considered to be the definitive edition.

This is an expensive, but absolutely invaluable publication, brought out by Cambridge University Press as part of this year’s bicentennial celebration and edited by Gordon Chancellor and John Van Whye (the same John Whye who maintains the complete works of Darwin online). It contains the entirety of Darwin’s handwritten journals of the voyage of HMS Beagle, written during the voyage. In it one can trace the development of Darwin’s revolutionary ideas as they first occurred to him, and see how the events of the voyage laid the groundwork for his revolutionary theories. This is a must-have edition for anyone who wants to understand how and when the Darwinian revolution began.

Charles Darwin was born on February 12, 1809, the same day as Abraham Lincoln. This propinquity of origins is all the more notable when one realizes that Darwin and his family were staunch abolitionists. Darwin himself tells how he became horrified by the institution of slavery while on the voyage of HMS Beagle. Desmond and Moore, whose 1994 biography of Darwin (Darwin: The Life of a Tormented Evolutionist, available here) is widely recognized as one of the best biographies of Darwin, have in this volume dug deeper into Darwin’s personal history, showing how his views on slavery and its abolition helped shape his views on the evolution of humans, as outlined in his Descent of Man.

Although perhaps the best known, Darwin’s round-the-world voyage aboard HMS Beagle was not by any means the only such voyage of discovery in the 19th century. Three of Darwin’s closest friends and collaborators in evolutionary biology — botanist Joseph Hooker, zoologist Thomas Henry Huxley, and professional collector and naturalist Alfred Russell Wallace — all participated in similar voyages, and all contributed to Darwin’s theories. McCalman describes all four voyages, and shows how the insights and information about natural history gained by these four great naturalists provided the foundation for the science of evolutionary biology in the 19th and early 20th centuries.

Quammen, David) (2007) The Reluctant Mr. Darwin: An Intimate Portrait of Charles Darwin and the Making of His Theory of Evolution. Atlas Books: New York, NY, ISBN 039332995X (paperback, $35.00), 304 pages. Available here.

Quammen’s biography of Darwin’s personal origin of the Origin is a perfect companion to Janet Browne’s two-volume biography of Darwin. Focusing on the period in Darwin’s life leading up to the original publication of the Origin, Quammen shows how Darwin’s personality and early education predisposed him to the intellectual and emotional labor that resulted in the publication of the Origin and its reception by the scientific community.

DARWIN'S LIFE AND WORK (children/school)

All too often people think that the work of great scientists such as Charles Darwin is only accessible to adults, especially scientists. Here is a brief selection of books for children, all published during this bicentennial year, which present Darwin and his work in a way that anyone, including young children, can understand and appreciate.Heiligman, Deborah (2009) Charles and Emma: The Darwins' Leap of Faith. Henry Holt and Co.: New York, NY, ISBN 0805087214 (hardcover, $18.95), 272 pages. Available here.

Heiligman’s biography of Charles and Emma Darwin begins with Charles drawing up a list of the pros and cons of marriage to his first cousin, Emma. His decision to marry her set in motion an emotional odyssey for Charles and Emma, who had very different views of religion. Charles’ theory of evolution threatened Emma’s deep religious belief, and forced Darwin to thoroughly document his views before publishing them. This sympathetic rendering of their happy, though sometimes turbulent, marriage is a wonderful introduction to the real life of a famous scientist, one that young adults will find particularly relevant to their own lives.

Lasky’s copiously illustrated account of Darwin’s life and work, focusing especially on his adventures while on the voyage of HMS Beagle, gives younger readers an engaging look at the work of the founder of the theory of evolution by natural selection. Lasky does not shy away from Darwin’s views on evolution and religion, presenting them in Darwin’s own words. The illustrations are particularly charming, rendered in various media in a quirky and engaging style.

Another illustrated account of Darwin’s life and work, this time covering his childhood, his adventures while on the voyage of HMS Beagle, and the subsequent development of his theory of evolution by natural selection. gives younger readers an engaging look at the work of the founder of the theory of evolution by natural selection. Illustrated with woodcuts and watercolor, McGinty and Azarian’s biographical history also touches on Darwin’s views on religion and philosophy in a way that is accessible to younger readers.

Schanzer’s illustrated account of Darwin’s voyage of HMS Beagle is more limited in scope than the others in this list, but succeeds in presenting Darwin’s natural history investigations in an engaging (and sometimes humorous) way. More like a graphic novel than a standard biography (complete with cartoon-like illustrations and speech balloons), Schanzer presents selected observations that led Darwin to his theory of evolution. Unlike the other three books for younger readers in this list, Schanzer avoids discussion of Darwin’s views on religion and philosophy, sticky strictly to the natural history of his historic voyage and the science that it inspired.

In addition to the books listed and reviewed here, those who are interested in the life and works of Charles Darwin can search Amazon.com, where most of the books listed above can be browsed, along with many others published in connection with the Darwin bicentennial. Books on the subject of evolution are listed here, including books both supportive of Darwin’s theory and critical of it.

I hope this list provides you with some ideas of how to celebrate Darwin's life and work by learning more about it.

Monday, November 09, 2009

Macroevolution: What Were the Evolutionary Ancestors of Whales?

ID supporters often assert that, although there is abundant empirical evidence for microevolution, there is no such evidence for macroevolution. One of the macroevolutionary transitions that they often cite is the evolution of whales from a land-dwelling ancestor. Which leads me to ask the following question:

What empirical evidence would verify (i.e. support) or falsify (i.e. undermine) the hypothesis that whales had evolved from a land-dwelling mammal? Please note that this is a hypothesis about macroevolution, not microevolution.

A basic principle of hypothesis validation in the natural sciences is that if one can find multiple lines of evidence, all of which support the hypothesis, then such evidence is much stronger than if there were only a single line of evidence. This is especially the case if the different lines of evidence are from very widely separated fields.

Until recently the main line of evidence for the evolution of whales (i.e. members of the mammalian order Cetacea) from even-toed ungulates (i.e. members of the mammalian order Artiodactyla) was anatomical. This anatomical evidence was derived from two sources:

1) similarities between the anatomy (especially skeletal anatomy) of living (i.e. "extant") Artiodactyls and Cetacea, and

2) an evolutionary phylogeny of the transition from terrestrial Artiodactyls to aquatic Cetacea, based on fossils.

Rather than summarize this comparative anatomical evidence here, I recommend that interested readers follow this link. What you will find is a fairly detailed summary of the evidence from comparative anatomy, all of it pointing to the conclusion that whales (i.e. Cetaceans) evolved from even-toed ungulates (i.e. Artiodactyls). It is this evidence that most evolutionary biologists have until recently cited as support for the macroevolutionary derivation of Cetaceans from Artiodactyl ancestors.

However, one can also ask the question Does the comparative genomics of Artiodactyls and Cetaceans support the same hypothesis? That is, are there observable DNA sequence similarities and differences that are similar in both scope and timing to the similarities and differences in the fossil record (and as reflected in the comparative anatomy of Artiodactyls and Cetaceans)?

This is an easily falsified hypothesis: If the genomic evidence does not support the Artiodactyl into Cetacean hypothesis — e.g. that Cetaceans evolved from some other clade, or that they had not evolved at all, but rather sprang into existence fully-formed and without genetic evidence of a macroevolutionary transition — then this evidence would not support the evidence from comparative anatomy and the macroevolutionary hypothesis based on comparative anatomy would be called into question.

So, what does the comparative genomic evidence indicate about the macroevolutionary relationships between the Artiodactyla and the Cetacea? Here’s a summary of the findings from comparative genomics:

The idea that whales evolved from within the Artiodactyla was based on analysis of DNA sequences. In the initial molecular analyses, whales were shown to be more closely related to ruminants (such as cattle and deer) than ruminants are to pigs. In order for the order name to reflect a real evolutionary unit, the term Cetartiodactyla was coined.

Later molecular analyses included a wider sampling of artiodactyls and produced a more complete tale. Hippos were determined to be the closest relative of whales, ruminants were related to a whale/hippo clade, and pigs were more distant. In addition to producing the controversial whale/hippo clade, these analyses debunked the idea that hippos and pigs are closely related. This had been a popular taxonomic hypothesis (Suiformes) based on similarities in morphological (physical) characteristics.

In addition to DNA and protein sequences, researchers tracked the movement of transposons called SINEs in the genome. A transposon is a DNA sequence that will occasionally make a copy of itself and insert that copy into another part of the genome. It is considered highly unlikely that SINEs will insert themselves into the exact same part of a genome by chance. The data indicate that several transposons inserted themselves at the same point in the genomes of whales, ruminants and hippos (sometimes referred to as "pseudoruminants" because although they have four-chambered stomachs like true ruminants, they do not chew the cud). This insertion point is not shared with camels and pigs.

This hypothesis has been tested with DNA sequences from a host of genes: the complete mitochondrial genome (as well as several of its genes independently), beta-casein, kappa-casein, von Willebrand factor, breast cancer 1, recombination activating genes 1 and 2, cannabinoid receptor 1, and several others. These sequence data and the transposons converge on the same conclusion that hippos and whales are more closely related to one another than either is to other artiodactyls.

Sequences analyzed in combined analyses with morphological characters have also produced the same results as sequences alone. Some have argued that the sheer number of characters (one for each nucleotide) in sequences swamps out the effects of morphology. There have been a few morphology-based studies that have suggested (weakly) the same results as the molecular results, but overall most morphological studies have conflicted with the whale/hippo hypothesis of Cetartiodactyla.

An important exception is a recent conducted by Boisserie et al. (2005). They examined 80 hard morphological characters of fossil and extant cetartiodactylan taxa. Their results suggest that hippopotamids evolved from within a clade of anthracotheres. That anthracothere/hippopotamid clade appears to be sister to the Cetacea and supports the molecular results.

[sources: http://en.wikipedia.org/wiki/Cetartiodactyla (summary article), where you can find links to many primary references]

Note that much of the genomic data (especially from transposon sequences) supporting the macroevolutionary hypothesis is based on non-adaptive DNA sequences. That is, DNA sequences that do not code for adaptive characteristics, and in many cases that do not code for anything at all. This is like figuring out which students have been copying the answers to test questions from other students by comparing their wrong answers. The right answers are the same for everybody, but wrong answers vary from student to student in virtually random ways. If two students have the same wrong answers, you can be reasonably confident that one of them copied the wrong answers from the other. You can then test this hypothesis by looking at seating charts, past test performance (cheaters are often identified by sudden increases in test scores without apparent increases in effort), and – often the last resort – asking them if they copied answers.

Is that all, or is there yet another line of evidence that might be pursued to verify or falsify the Artiodactyl into Cetacean hypothesis? Yes, there is. Consider the observable fact that whales reproduce much more slowly than even-toed ungulates (such as deer and hippos). Indeed, there is a general principle in zoology that the larger the members of a species are (on the average) the fewer offspring they have, the more widely spaced those offspring are in time, the fewer offspring they can have over their lifetime, and the longer the average lifespan of individuals.

For example, deer can have offspring every year, and under good conditions can sometimes have twins or even triplets in one reproductive cycle. By comparison, baleen whales can only have offspring every few years (it can take up to two years for one pregnancy in large baleen whales), they virtually never have more than one calf at a time, they have only a few reproductive life cycles per lifetime, and they have much longer lifespans than deer.

This means that, if Cetaceans evolved from Artiodactyls, one might be able to find empirical evidence that the rate of the macroevolutionary transition from Artiodactyl ancestors into Cetacean descendants had slowed down as the result of the increase in size, decrease in number of offspring per reproductive cycle, decrease in total number of offspring per lifetime, and increase in average lifespan. In brief, there might be evidence that the macroevolutionary “clock” slowed down as Cetaceans evolved larger and larger size.

ABSTRACT: Baleen whales are the largest animals that have ever lived. To develop an improved estimation of substitution rate for nuclear and mitochondrial DNA for this taxon, we implemented a relaxed-clock phylogenetic approach using three fossil calibration dates: the divergence between odontocetes and mysticetes approximately 34 million years ago (Ma), between the balaenids and balaenopterids approximately 28 Ma, and the time to most recent common ancestor within the Balaenopteridae approximately 12 Ma. We examined seven mitochondrial genomes, a large number of mitochondrial control region sequences (219 haplotypes for 465 bp) and nine nuclear introns representing five species of whales, within which multiple species-specific alleles were sequenced to account for within-species diversity (1-15 for each locus). The total data set represents >1.65 Mbp of mitogenome and nuclear genomic sequence. The estimated substitution rate for the humpback whale control region (3.9%/million years, My) was higher than previous estimates for baleen whales but slow relative to other mammal species with similar generation times (e.g., human-chimp mean rate > 20%/My). The mitogenomic third codon position rate was also slow relative to other mammals (mean estimate 1%/My compared with a mammalian average of 9.8%/My for the cytochrome b gene). The mean nuclear genomic substitution rate (0.05%/My) was substantially slower than average synonymous estimates for other mammals (0.21-0.37%/My across a range of studies).

CONCLUSION: The nuclear and mitogenome rate estimates for baleen whales were thus roughly consistent with an 8- to 10-fold slowing due to a combination of large body size and long generation times. Surprisingly, despite the large data set of nuclear intron sequences, there was only weak and conflicting support for alternate hypotheses about the phylogeny of balaenopterid whales, suggesting that interspecies introgressions or a rapid radiation has obscured species relationships in the nuclear genome. [emphasis added]

So, there are indeed empirically falsifiable hypotheses for the macroevolution of whales from land-dwelling ancestors. If whales (Cetacea) evolved from even-toed ungulates (Artiodactyla), then the following predictions should be supported by the observable data:• that there should be anatomical similarities between extant Artiodactyls and Cetaceans,• that there should also be anatomical similarities between fossil Artiodactyls and Cetaceans,• that there should be shared similarities and differences between the genomes of extant clades of Artiodactyls and Cetaceans, and that the overwhelming majority of these similarities and differences would mirror the comparative anatomical evidence for the macroevolutionary origin of the various clades of the Cetartiodactyla, and • that the inferred slowing of macroevolutionary change during the transition from Artiodactyl ancestors to Cetacean descendants should also be consistent with the hypothesis that the rate of this transition would have slowed as the result of increasing body size, increasing reproductive spacing, decreasing numbers of offspring per life cycle, and increasing longevity.

And it is.

Clearly, an ID supporter might then ask for specific empirical evidence on how the various transitions occurred at the genetic and developmental level, and if these details could unambiguously distinguish between natural and supernatural causes for such genetic mechanisms. Evolutionary developmental biologists are currently working on answers to the first part, but I personally cannot imagine how one could empirically test the second part. Furthermore, it seems to me that invoking a supernatural cause for the macroevolutionary transition from Artiodactyls to Cetaceans would be unnecessary, and would add nothing whatsoever to our understanding of the mechanisms by which this transition occurred.

Ergo, if I were doing this research and publishing my results I wouldn’t mention it, as it would be completely unnecessary for a scientific explanation of this phenomenon.

Just out of curiosity, ask yourself how one might use any of the foregoing as positive or negative empirical evidence for the existence of God. I mention this because some evolutionary biologists believe they can use the data of evolutionary biology to disprove the existence of God, and some ID supporters believe they can use the data of evolutionary biology to prove the existence of God. Personally, I believe both attempts are misguided, pointless, and ultimately futile. That’s why I don’t make such attempts, and wonder why anyone would.